Friday, June 29, 2012

In his book Inside the Human Genome evolution professor and National Academy of Science member John Avise continues with the usual evolutionary religious claims that the evil and inefficiency of biological designs—at the molecular level in this case—necessitate evolution, for such designs would never have been designed or created by a loving higher intelligence. As usual, it’s all about religion.

In his chapter on non intelligent design, Avise points out that the world is deeply flawed right down to the fundamental, molecular level, and he repeats his religious belief that ascribing such a world to a Creator God is tantamount to blasphemy:

If, on the other hand, natural causation is denied, and a caring Intelligent Designer is to be held directly responsible for life’s imperfect features, then the theodicy challenge remains poignant. How could a Creator God have engineered such a deeply flawed biological world, right down to its most elemental molecular features? Unless we pretend that biological defects do not exist, we seem forced to conclude that any Intelligent Designer is either technically fallible, morally challenged, or both. Furthermore, if the intelligent designer is deemed to be the Abrahamic God (rather than a Martian, for example), then are we not guilty of blasphemy in ascribing to Him a direct hand in sponsoring the molecular genomic flaws that plague human health? [156]

But this is only the beginning of evolution’s metaphysics and Avise next points out that these so-called “shared errors” are common to many species:

Furthermore, molecular imperfections in the human genome provide significant evidence for evolution not only because they are imperfect but also because they are phylogenetically interpretable. Most genomic flaws (apart from de novo mutations that are currently confined to particular individuals) are distributed across biological taxa in ways that make evolutionary (i.e., phylogenetic) sense. This is true at all levels in the phylogenetic hierarchy. At the microevolutionary scale, many genetic disorders in humans “run in families” according to specifiable rules of Mendelian inheritance. [157]

Avise’s argument that genetic disorders “run in families” is weak. Nor is his argument from shared errors any better because convergence in biology is rampant. Evolutionists never had a problem before with astonishingly complex designs that are found in distant branches of the evolutionary tree.

If evolution is true those designs must have evolved independently, in spite of the ridiculously low chances of such an evolutionary path occurring twice (or even once for that matter).

So if evolution has no problem with biology’s astonishing levels of convergence, which repeatedly falsified evolutionary expectations, then it hardly can claim some other similarities, flawed or otherwise, as compelling evidence.

But of course this isn’t where the power of the argument comes. The point of the argument, as Avise immediately explains, is a religious one:

And at the mesoevolutionary and macroevolutionary scales, humans share many molecular features, including particular molecular flaws, with various other taxa in the nested hierarchies of phylogeny. When fine details of molecular errors recur in phylogenetically related species, special-creation explanations for such errors are thus effectively eliminated (unless we are to suppose that a bumbling Creator made the same molecular mistakes time and again when directly forging different species). [157]

Evolutionary thought has always been a referendum on creationism. That’s why they insist on labeling ID theorists as “creationists.”

Let’s be clear about the nature of this debate. There is nothing wrong with evolutionary theorizing, per se. For there is nothing wrong with religious premises driving one’s thinking. Men have done this for eons and it certainly is not showing any signs of slowing.

Evolutionary thought can be traced to antiquity. In the era of modern science it shows up in the seventeenth century in Christian thinkers such as Malebranche, Burnet, Ray, Cudworth, and Leibniz, to name a few.

By the nineteenth century this movement had gained substantial momentum. Darwin served to collect, formalize and apply this thought specifically to the origin of species and his work was drenched in metaphysics. He is rightly exalted as the father of modern evolutionary thought as he set the template for the historical sciences in the twentieth century.

Most importantly, Darwin refined and exemplified a method that is now taken for granted in origins research. Namely, Darwin’s thought was motivated by, entailed and hinged on metaphysics no less than earlier thinkers. But in Darwin the metaphysics was subtly dressed in empirical language. Here is a typical example:

Thus, we can hardly believe that the webbed feet of the upland goose or of the frigate-bird are of special use to these birds; we cannot believe that the similar bones in the arm of the monkey, in the fore-leg of the horse, in the wing of the bat, and in the flipper of the seal, are of special use to these animals. We may safely attribute these structures to inheritance.

One can read through such passages and almost conclude that Darwin is merely presenting empirical scientific reasoning and conclusions. And so it is with today’s evolutionary reasoning, such as this typical textbook example:

If the 11 species had independent origins, there is no reason why their [traits] should be correlated.

It all sounds so scientific. But of course it is not. This is the great deception of evolutionary thought. It is made to sound scientific, and indeed evolutionists argue strenuously that it is. They claim the high ground of “just science” and use creationists as their foil.

And so there are three problems with evolutionary thought. First, it claims that its finding that evolution is a fact derives from empirical science. Second, it criticizes the use of religious assumptions. Third, its everything-came-from-nothing hypothesis, while religiously compelling, is scientifically absurd.

The first of these problems is a lie. The second is a hypocrisy. And the third is an abuse of science.

Evolutionists, of course, recognize none of this. But neither do their detractors. Common criticisms are that evolution is “only a theory” and so could be wrong. Even more typical is the complaint that evolution is really nothing more than atheism in disguise. Both criticisms are glaring misconceptions of evolutionary thought which simply give evolutionists more confidence. If criticisms of their ideas are clearly false, then they must be doing well.

This is why it is important to understand evolution. For both evolutionists and skeptics, progress will be difficult until evolution is properly understood.

Thursday, June 28, 2012

When Charles Darwin proposed his theory of evolution in 1859 there were many scientific problems with the idea. Today, a century and a half later, we know of a great many more empirical challenges to the idea that the species arose spontaneously. The latest falsified expectation is that microRNAs, discovered only a few decades ago, when compared between different species do not align with the evolutionary tree. Evolutionist Kevin Peterson and colleagues are pursuing this research. “I've looked at thousands of microRNA genes,” explains Peterson, “and I can't find a single example that would support the traditional tree.”

While there remain questions about these new phylogenetic data, “What we know at this stage,” explains another evolutionist, “is that we do have a very serious incongruence.” In other words, different types of data report very different evolutionary trees. The conflict is much greater than normal statistical variations.

“There have to be,” adds another evolutionist, “other explanations.” One explanation is that microRNAs evolve in some unexpected way. Another is that the traditional evolutionary tree is all wrong. Or evolutionists may consider other explanations. But in any case, microRNAs are yet another example of evidence that does not fit evolutionary expectations. Once again, the theory will need to be modified in complex ways to fit the new findings.

It isn’t that any one particular finding falsifies evolution, but the consistent pattern of contradictory findings—from nature’s complexities to uncooperative patterns—show that evolution is not explanatory, but rather tautological.

If you thought that Harold Zakon’s blunder in the very first sentence of his new PNAS paper, on the evolution of voltage-gated sodium channels, was merely the obligatory secret handshake and that thereafter Zakon would get down to business with some real science, well, think again. After his rather shaky start you’ll find that the second sentence is even worse than the first:

The nervous system and muscles evolved shortly thereafter.

Zakon gives no citation on this claim. Apparently it is one of evolution’s brute facts which evolutionists need merely to remind themselves of occasionally.

Later Zakon does admit to some problems with the evolutionary tree:

The phylogeny of basal metazoans is poorly resolved, likely because of the rapid radiation of these then-new life forms

So not only did metazoans just happen to arise spontaneously, but they did so in a “rapid radiation.” For every failure of evolutionary theory you can bet there are always the usual explanatory devices competing to fill the gap.

Not bad for something from nothing. As you can see, that just has random mutations written all over it. After all, such molecular engineering marvels just “appear” at some long lost unobservable time and place:

Potassium leak and voltage-dependent K+ (Kv) channels appeared three billion years ago in bacteria and occur in all organisms

Potassium channels “appeared” three billion years ago? For this claim Zakon cites a paper written by evolutionists who presuppose that potassium channels (and everything else for that matter) evolved. In other words, to support his unscientific assertion that potassium channels “appeared” three billion years ago, Zakon cites the work of evolutionists who assume that potassium channels “appeared” at some point.

Just when you thought this evolutionary tale could not become any more bizarre, Zakon explains how he believes these potassium channels “appeared”:

Kv channels are the “founding members” of the family of ion-permeating channels whose basic structure is a protein of six transmembrane helices (6TM) that associate as tetramers to form a channel. At some point early in eukaryote evolution, the gene for a 6TM channel likely duplicated, giving rise to a protein with two domains. These proteins then dimerized to form a complete channel. Such a channel still exists in the two-pore channel family of Ca2+-permeable channels localized in endosomes and lysozomes. The gene for a two domain channel likely duplicated to make a protein with four domains capable of forming a channel on its own (4x6TM). Eventually such a four-domain channel evolved (or retained) permeability to Ca2+, and these handily became involved in intracellular signaling. Other Ca2+-binding proteins and enzymes first appeared in single-celled eukaryotes. Additionally, there are single 6TM Na+-permeable channels in bacteria. Their relationship to eukaryotic [sodium] channels is unclear, and they will not be discussed in this review.

In the world of an evolutionists, astronomically complex structures just happen to form spontaneously. Things appear, duplicate, modify, retain, evolve, serendipitously perform new functions, and so forth.

Zakon goes on to explain that calcium channels also “appear early in animals.” Furthermore, it has been confirmed that sodium channels evolved from calcium channels. And how could evolutionists make such an astonishing discovery? Easy, by comparing the structures and amino acid sequences of these marvels, such as in choanoflagellates:

Analysis of putative Cav and Nav channel genes from fungi, choanoflagellates, and metazoans confirm this speculation and show that choanoflagellates have a channel that groups with recognized [sodium] channels with strong support.

Though they cannot explain how even a single protein could evolve, evolutionists conclude that voltage-gated sodium channels evolved from calcium channels because they share certain similarities.

Later we learn that a variety of key molecular components were luckily finally in place “for construction of the nodes of Ranvier.”

And that electric organs evolved independently in African and American fish as the sodium channel gene “underwent a burst of evolutionary change at the origin of both groups of electric fishes, with numerous substitutions in key regions of the channel.”

Then there are the various neurotoxins, such as tetrodotoxin, that interfere with the sodium channel. Vertebrates that maintain high concentrations of tetrodotoxin must somehow protect their several types of sodium channels from the dangerous poison.

For example, hundreds of fish species, such as the Pufferfish, safely maintain high concentrations of tetrodotoxin with sodium channel genes that have slight differences which help to make the fish immune to tetrodotoxin. But how could these similar differences have evolved in all these different fish species? The slow process of random mutations would require too much time to save a species from its internal poison. Furthermore these modifications would be required in not just one, but all the different sodium channel genes. Once again evolution has an explanatory device:

We still do not know how pufferfish were able to survive with only one or a few tetrodotoxin-resistant [sodium] channels. The most likely scenario is that tetrodotoxin-resistant mutations accumulated gradually in the [sodium] channel genes as fish were initially exposed to a light load of tetrodotoxin. Gradually, as more channels gained resistance, they were able to carry a greater toxic load.

There is always a just-so story.

Then there are the garter snakes and their prey, the newts. Newts maintain high concentrations of tetrodotoxin and garter snakes that eat them have sodium channel genes with the right, immunizing, modifications.

But garter snakes that live in different areas do not have these modifications, and may die if they ingest a newt. In fact it appears that the different garter snakes populations that prey on newts would have had to independently evolve their sodium channel modifications:

Even more striking, tetrodotoxin resistance has evolved multiple times in populations of other species of garter snakes that are also sympatric with newts in the Pacific Northwest and California, as well as other snake species sympatric with other newts or frogs that use tetrodotoxin in South America and Asia.

But that’s not all. The newt larvae do not produce the tetrodotoxin poison but since the adult newts can be cannibalistic the larvae will flee when they smell tetrodotoxin nearby. So in this case tetrodotoxin is a chemical signal. This is also true in pufferfish when males detect nanomolar levels of tetrodotoxin resulting from female egg laying.

This is all fascinating biology and ion channels, such as these voltage-gated sodium channels, are incredible molecular machines. And while it is true that all of this can be explained in a speculative evolutionary narrative, the story here is that, as usual, the biology does not easily fit evolutionary theory. Papers such as this one are cited as yet more confirmations of evolutionary theory, but in fact they are little more than evolutionary story-telling.

Wednesday, June 27, 2012

You won’t believe Harold Zakon’s fallacy in the very first sentence of his new PNAS paper on sodium channel evolution. The University of Texas evolutionist writes:

Multicellular animals evolved >650 million years ago (1).

And what is Zakon’s reference for this rather remarkable claim? It is a 2009 Naturepaper on fossilized steroids indicating ancient multicellular life. Amazingly, Zakon conflates existence with evolution. In other words, whatever appears in the fossil record must have evolved.

And who allowed this colossal, non scientific, blunder into print? None other than John Avise who just happens to believe that it would be blasphemous to ascribe harmful and inefficient genomic designs to God.

In a massive exercise of drinking their own bathwater, evolutionists peer-review and edit papers written by other evolutionists and the result is, quite literally, garbage out.

Tuesday, June 26, 2012

Last weekend evolutionists fired off another round of metaphysics and as usual there was no counter attack. From their hilltop position evolutionists are free to throw down their religious mandates with impunity while the low-landers do nothing but run for cover. This time it was astrophysicist Alex “Philo” Filippenko lighting off the Infinite Regress howitzer from that bastion of Enlightenment, the SETICon 2 conference in Silicon Valley. Filippenko first fired a shot across the bow with his statement that “The Big Bang could’ve occurred as a result of just the laws of physics being there.” That had the Philistines cheering and the low-landers complaining as the evolutionist had left them with nothing but the laws of physics. That’s when Filippenko brought out the big gun and demolished even that last foothold:

"The question, then, is, 'Why are there laws of physics?'" he said. "And you could say, 'Well, that required a divine creator, who created these laws of physics and the spark that led from the laws of physics to these universes, maybe more than one.'"

But that answer just continues to kick the can down the road, because you still need to explain where the divine creator came from. The process leads to a never-ending chain that always leaves you short of the ultimate answer, Filippenko said.

The origin of the laws of physics remains a mystery for now, he added, one that we may never be able to solve.

"The 'divine spark' was whatever produced the laws of physics," Filippenko said. "And I don't know what produced that divine spark. So let's just leave it at the laws of physics."

In other words, we must avoid the dreaded infinite regress. This of course is straight from the pen of David Hume whose character Philo fired off this weapon centuries ago:

How, therefore, shall we satisfy ourselves concerning the cause of that Being whom you suppose the Author of Nature, … if we stop, and go no further; why go so far? why not stop at the material world? How can we satisfy ourselves without going on in infinitum? And, after all, what satisfaction is there in that infinite progression?

Or as evolutionist Mark Ridley put it:

Positing a God merely invites the question of how such a highly adaptive and well-designed thing could in its turn have come into existence. Theological sophistry about the perfect simplicity of God and the inexplicability of the First Cause can be ignored here: the problem is to explain adaptive complexity. The first alternative to natural selection, therefore, is a viciously circular argument, and unscientific.

For Hume and the evolutionists there are two possibilities: Design and complexity arise on their own via natural law, or there is an infinite regress of “designers.”

Given these two absurdities the evolutionists, of course, choose law. But this is not the key move, for at this point the metaphysical fire fight is long over. The key move—and metaphysical heavy lifting—came at the earlier stage where the alternatives were defined. Remember, he who defines the debate wins the debate.

Science doesn’t tell us that there are two possibilities. It doesn’t tell us that design and complexity either arose on their own or else there is an infinite regress of designers. That is a metaphysical assertion—one of many that underwrite the evolution research program.

Amazingly evolutionists claim they are just “doing science” as they fire off these metaphysical salvos. Religion drives science, and it matters.

Saturday, June 23, 2012

Proteins perform a wide variety of tasks in the cell and when a particular job needs to be done the right protein is quickly synthesized by unwinding the right DNA gene, making a copy, editing the transcript, and translating the transcript, according to the DNA code, into a sequence of amino acids. Evolutionists had no explanation for this incredible and profound molecular manufacturing system (which still out performs anything scientists can come up with), but they remained steadfast. Indeed they argued all of this provided yet more proofs for evolution. Why? Because the DNA code was essentially universal. As one evolutionist explained, while the genetic code is preserved across species, it would not be if the species had been created independently. [1] If that’s true then the genetic code must have somehow evolved. Is that true? It’s difficult to say because that is, as usual, a non scientific claim. But aside from the metaphysics and the unexplained molecular manufacturing system, there is another problem with this story. It has now turned out to demolish evolutionary theory and has left evolutionists staring into the headlights.

Years after the universal DNA code was discovered, several other codes were also discovered which were not only astonishingly complex, but they were not universal. One such code is the so-called splicing code.

In higher organisms many of the genes are broken up into expressed regions, or exons, which are separated by intervening regions, or introns. After the gene is copied the transcript is edited, splicing out the introns and glueing together the exons. Not only is it a fantastically complex process, it also adds tremendous versatility to how genes are used. A given gene may be spliced into alternate sets of exons, resulting in different protein machines. There are three genes, for example, that generate over 3,000 different spliced products to help control the neuron designs of the brain.

And how does the splicing machinery know where to cut and paste? There is an elaborate code that the splicing machinery uses to decide how to do its splicing. This splicing code is extremely complicated, using not only sequence patterns in the DNA transcript, but also the shape of transcript, as well as other factors.

What is also complex about the new code is that it is context-dependent. In fact it even varies in different tissue types within a species. And studies of RNA binding proteins show even more complexity. These proteins are part of the molecular splicing machinery and they often regulate each other leading to an “unprecedented degree of complexity and compensatory relationships.” As one researcher explained:

We identified thousands of binding sites and altered splicing events for these hnRNP proteins and discovered that, surprisingly these proteins bind and regulate each other and a whole network of other RNA binding proteins.

Regulate each other and a whole network of other RNA binding proteins? Needless to say there is no scientific explanation for how this marvel could have evolved. And since this code is not universal but, quite the opposite, highly varying even between tissues, we can safely conclude the “universal code” prediction of evolution is falsified.

If evolution is true then we expect codes to be universal. Here we have an obvious example of a code that most definitely is not universal, so the prediction is false. And if a prediction is false, then either the theory is false, or it must be modified. But with so many falsifications, and so many modifications that make no sense on evolution, it is obvious that something is very wrong with the theory. In this case we would have to say that random mutations just happened to create many different splicing codes, over and over, of unimaginable complexity.

Thursday, June 21, 2012

Remember when evolution was a fact? Remember when your high school biology teacher explained the origin of life from a muddy pond (or maybe ocean vent) was beyond any doubt? Remember when the National Academy of Science declared that “For those who are studying the origin of life, the question is no longer whether life could have originated by chemical processes involving nonbiological components. The question instead has become which of many pathways might have been followed to produce the first cells”? [1] Remember when Carl Zimmer wrote that scientists “have found compelling evidence that life could have evolved into a DNA-based microbe in a series of steps.”

Well, err, that was all wrong. Truth be told, there never was any such compelling evidence. There never was any proof that life arose spontaneously—from a warm little pond, ocean vent, or anywhere else for that matter.

In fact, as one evolutionist admitted, “there's not even a consensus on how to approach the problem.” That doesn’t exactly qualify as a fact.

1. National Academy of Sciences, Science and Creationism: A View from the National Academy of Sciences, 2d ed. (Washington, D.C.: National Academy Press, 1999) 6.

Sunday, June 17, 2012

As reported at Evolution News and Views: It is said that a picture speaks a thousand words. An animation speaks at least 10,000.

This animation illustrates a few of the amazing operations that take place in living organisms. Wise men from ages past could only dream of such things but now that we know it evolutionists preach that it is meaningless. They are blind guides who, while professing to be wise, have become fools.

In his book Inside the Human Genome Evolution professor and National Academy of Science member John Avise continues with the usual evolutionary religious claims that the evil and inefficiency of biological designs—at the molecular level in this case—necessitate evolution, for such designs would never have been designed or created by a loving higher intelligence:

Approximately 0.1% of humans who survive to birth carry a duplicon-related disability, meaning that several million people worldwide currently are afflicted by this particular subcategory of inborn metabolic errors. Many more afflicted individuals probably die in utero before their conditions are diagnosed. Clearly, humanity bears a substantial health burden from duplicon-mediated genomic malfunctions. This inescapable empirical truth is as understandable in the light of mechanistic genetic operations as it is unfathomable as the act of a loving higher intelligence. [112]

There you have it. Evil exists and a loving higher intelligence wouldn’t have done it that way. It is a powerful argument for evolution, but its power comes from religion, not science. And that is the story of evolution. From the pre Darwin Enlightenment years to today, these metaphysical arguments have mandated an evolutionary narrative. But the science reveals monumental problems. What Darwin and the evolutionists have done is to manipulate the science to fit our religious requirements. Theology is, and always has been, the queen of the sciences.

Saturday, June 16, 2012

The religious beliefs of evolutionists mandate that evolution, in one form or another, must be true. The details of how it happened don’t matter, but their religion demands that the world arose on its own. These beliefs have been clearly stated and proclaimed for centuries. And these beliefs have been proclaimed by a wide variety of believers, including Anglicans, Lutherans, Roman Catholics, Jews, agnostics and atheists. Evolution is, if anything, a religious theory and there is nothing wrong with that. But evolutionists deny any such religious influence and criticize others for undue religious biases. That reveals the hypocrisy of evolutionary thought and a monumental internal contradiction.

As a general rule, those who are convinced they are free of metaphysics are those who are most beholden to metaphysics. P.Z. Myers, for example, wrote in the LA Times that he is “pretty certain that if there were an all-powerful being pulling the strings and shaping history for the benefit of human beings, the universe would look rather different than it does.”

That is a religious claim.

But when I pointed this out an evolution professor accused me of deception and asserted that Myers made no such religious claim:

see what the charlatan has done here: Myers said "IF there were an all-powerful being..."

But the confidence man's trick was to turn that conditional into a non-conditional statement. Keep you eyes out: It's his chief modus operandi.

No metaphysics committed here by Myers, once you peek behind the curtain.

The hypocrisy just keeps on coming. Evolutionists make religious arguments that mandate evolution, they accuse others of what they do, and when you point it out they just bring more empty accusations and denials. In this case, the evolution professor attempts to hide the religion with the fallacious argument that Myers argument is not a religious claim because it is a conditional. Of course that makes it no less of a religious claim. Religion drives science, and it matters.

As a general rule, those who are convinced they are free of metaphysics are those who are most beholden to metaphysics. Evolution professor and atheist P.Z. Myers once explained in an LA Times piece that he is “pretty certain that if there were an all-powerful being pulling the strings and shaping history for the benefit of human beings, the universe would look rather different than it does.” Pretty certain God wouldn’t have made this world? Myers is known for his strident views and he probably has never stopped for a moment to ponder the rather awkward question of how he knows of that certainty. For while Myers criticizes others for their religious beliefs, Myers’ notion of how the universe would and would not look if such an all-powerful being created it is, itself, a religious belief. Perhaps Myers’ certainty is at the 99% level. How did he arrive at such a value? You see whether Myer’s certainty is 99%, 98%, 90%, or whatever, does not matter. For in any case, it is a religious claim. There is no scientific experiment or evidence to back up Myers’ belief. There is no logic or rationale to which Myers could appeal. In fact not only is Myers’ criticism of religious beliefs hypocritical, but Myers own position is fallacious as it entails a massive internal contradiction. To wit, Myers concludes with atheism, but his very atheism undermines his religious claim. If atheism were true, then no religious claims could be known to be true. Simply put, religious claims would be meaningless. One could claim there is a 99% chance God would or would not do this or that, but such a claim would be worthless. Hypocrisy and irrationality are signs of the worst side of religion. He was brought up a Lutheran but Myers is now a religious fundamentalist.

And so it is something of a stretch for Myers to claim his high claims for evolution are objective, scientific conclusions. After all, if one is an atheist then evolution is pretty much the only alternative.

In fact Myers irrationality was on further display this week when he wrote that he is certain of evolution because it “occurred” and after all, it hasn’t been falsified:

I am certain that evolution occurred. The evidence is in; the process occurred and is occurring, there are no known barriers to natural processes producing modern life from proto-life/chemistry over the course of 3.8 billion years, and all the evidence we do have shows modern forms being incrementally modified versions of earlier forms. We don’t know all the details, of course, and just maybe someone somewhere could discover a real hurdle that could not have been overcome without intelligent aid, but I know for a fact that no creationist has ever come up with a defensible objection, and that nearly all the creationists who pontificate so ponderously on the impossibility of biology, Plantinga among them, always turn out to be profoundly ignorant of the science. There’s a good inverse correlation between knowledge of biology and certainty that evolution can’t work.

Notice the irrational leap evolutionists always take. In science theories are not true simply because they have not been disproven, but Darwin changed all that. These days Myers and evolutionists operate from a very low burden. Evolution is a fact unless it is falsified to their satisfaction.

So while evolution fails one prediction after another, and while evolutionists are continually surprised by the evidence, and while evolutionists cannot even come close to explaining how evolution occurred, Myers nonetheless is convinced. After all, the process occurred and no creationist has ever falsified it.

Myers is a beholden to his metaphysics. He is a religious fundamentalist and his fundamentalism has led to him to the age-old sophistry that everything must have arisen from nothing, and that’s a fact.

Friday, June 15, 2012

Evolution Professor Jerry Coyne, who believes all of biology spontaneously arose by itself, has done it again. Coyne insists evolution is a fact, and like all evolutionists he has plenty of religious reasons for his confidence which he gives after blaming creationists for religious reasoning. And like all evolutionists he misrepresents science, such as when he claims that “All vertebrates begin development looking like embryonic fish because we all descended from a fishlike ancestor with a fishlike embryo. We see strange contortions and disappearances of organs, blood vessels, and gill slits because descendants still carry the genes and developmental programs of ancestors.” Of course that isn’t true, but Coyne has once again gotten away with it, this time with the help of a fancy new blog from an NCSE member.

The NCSE member says it’s perfectly fine to misrepresent science and say mammalian embryos have gill slits because, after all, evolutionists have been doing this all along and even before Darwin, natural theologians noted the strong similarities between mammalian and fish embryos. So when the field was in its infancy naturalists noted such similarities so now, two centuries later, it’s OK to say mammalian embryos have gill slits even though they don’t.

Whatever. Coyne escapes again with a fast one, and certainly is happy about it. He calls it a “wonderful new post” which takes those creationist rascals “completely apart” and it is “really educational.”

Not surprisingly, of course, this “wonderful” new post has all the usual misrepresentations (embryology “remains one of most compelling subsets of evidence for evolution”) and fallacious similiarity-implies-evolution reasoning (“We can, informally, call pharyngeal clefts ‘gill slits’ in the same way we call kiwi ‘wings’, wings, or cetacean
‘limb buds’, limb buds, because despite the fact they no longer develop into functioning wings, limbs, or gills, in the organisms that bear them, because they are clearly homologous to those characters in organisms where they do retain those functions.”) so familiar to Coyne.

Most important though are the non scientific, religious mandates that underwrite evolution. You can see some of Coyne’s examples here, here, here, here and here. Misrepresentations and fallacies hardly matter when your religion tells you evolution must be true.

In this “wonderful” new post there is the venerable argument from dysteleology and its poster child example, the giraffe recurrent laryngeal nerve which is “of comic proportions” and makes “no obvious sense.” And there is the obligatory argument from the intellectual necessity of evolution. After all, “what is their [creationists] explanation for this pattern of embryological similarities amongst vertebrates that develop into very different adults?” And saying such similarities are a consequence of design is no better:

In reality their use of the term “common design” does nothing but relabel our ignorance. Worse it creates whole new sets of unanswerable questions. Designed by whom? Was it one designer or many (as in car companies)? How did he/she/it/they implement their design? Why did they design things the way they did? Why did they implement their designs in the timetable that they did? And on and on.

It gets worse if the “designer” is transcendent and omnipotent. This makes the concept completely untestable (and therefore unscientific) as such a creator could create anything, in any way, for reasons known only to itself.

Without evolution, there simply is “no coherent, testable, alternative explanation.”

So there you have it. Once again the evolutionist gets away and evolution wins the day. Evolution must be true, we may have no idea how such heroics occurred, but we certainly know that they did occur. Our religion demands it.

Thursday, June 14, 2012

You’ve seen evolutionists falsify the science and you’ve seen their religious mandates, but as the contradictions mount now they are simply referencing their unpublished data. In a study dealing with genetic regulation, the evolutionists discovered even more incredible complexity at the messenger RNA level. Here is how one writer summarized the results:

A team of molecular biologists from Cold Spring Harbor Laboratory (CSHL) has now discovered that mRNAs can be targeted for destruction by several modes and molecules, highlighting a previously unanticipated complexity in the control and regulation of the cell's genetic messages.

As with the previously known genetic regulation mechanisms, evolutionists can offer nothing more than vague speculation about how such incredible complexity could have arisen spontaneously. One of the proteins involved in some aspects of this regulation is called Ago and the evolutionists make the rather heroic claim that this protein, as found in mammals, evolved from an earlier version that was in ancient vertebrates. As a reference for this jaw-dropping, unscientific, claim, they unbelievably cite their “unpublished data”:

The four mammalian Ago homologs evolved from a common ancestor early in the vertebrate lineage (our unpublished data).

Imagine a physicist claiming to have proven perpetual motion and citing his unpublished data. This isn’t even wrong. Nor do terms such as absurd or ludicrous do justice to such inanity. Nothing in biology makes sense in the light of evolution.

In his book Inside the Human Genome Evolution professor John Avise makes the usual evolutionary truth claims that biological designs make “no (theo)logical sense” and “defy notions of a supreme intelligence.” The biological designs, in this case, are those involved in the mitochondria’s cellular energy production. Avise writes:

Considering the critical role of cellular energy production in human health and metabolic operations, why in the world would an intelligent designer have entrusted so much of the production process to a mitochondrion, given the outrageous molecular features this organelle possesses?. Why would a wise designer have imbued mtDNA with some but not all of the genes necessary to carry out its metabolic role (and then put the remaining genes in the mucleus instead)? Why would a wise engineer have put any crucial genes in a caustic cytoplasmic environment where they are exposed routinely to high concentrations of mutagenic oxygen radicals? And why would He have dictated that the mitochondrial genetic code must differ from the nuclear genetic code, thereby precluding cross-translation between two genomes for which effective communication would seem to be highly desirable?
The puzzlement for explanations involving ID goes even further. Why would an intelligent designer have engineered mtDNA structures (such as a closed-circular genome, no introns, no junk DNA, lack of binding histones) and mtDNA operations (such as little or no genetic recombination, the production of a polygenic transcript, a limited ability to mend itself, and no self-sufficiency in transcription or translation) to differ so fundamentally from their counterpart features in the nuclear genome? In a nutshell, the underlying design of the whole mitochondrial operation seems to make no (theo)logical sense. Not only is the overall design of mtDNA suboptimal—it is downright ludicrous. [103-4]

However, as discussed in chapter 1, in this book we are not particularly concerned with genomic features that suggest good workmanship because such features are philosophically consistent with either natural selection or intelligent causation. Our focus instead is on genomic features that defy notions of a supreme intelligence underlying biological design. Genomic flaws should in principle provide a more decisive test of whether unconscious evolutionary processes or cognitive agents have shaped our genes. [108]

Evolutionists have been making these arguments for centuries but what many observers, including historians and philosophers of science, fail to realize is that these arguments are metaphysical. One reason for this failure is that these evolutionary claims are rather charged and polarizing. People tend to agree or disagree with them, and hence the debate rapidly focuses on whether or not evolutionary claims are true.

While certainly that is an interesting question and worthy of discussion at some point, it misses the more fundamental point which is that evolutionary thinking is metaphysical. It may be true, it may be false, but it is metaphysical.

The claim that evolution is overwhelmingly a fact is underwritten not by the science (on which evolution is problematic), but by the metaphysics. For instance, set the debate aside for a moment and take the evolutionary position. Assume, for a moment, that you believe what evolutionists believe. Pretend that you, rather than the evolutionist, wrote the above passages. Now ask yourself, is evolution a fact?

Of course it is. It must be. Once you understand evolutionary thinking, then you will understand why they say evolution is a fact. Evolutionists claim the high ground of science and accuse others of religious bias. But it is all a hypocritical lie.

And when confronted with this evolutionists equivocate on their claims. They say the “fact” of evolution refers merely to change over time. That equivocation is easily exposed and it reveals how twisted is evolutionary thinking. Oh what a tangled web we weave.

Tuesday, June 12, 2012

We have seen that an evolution professor and member of the National Academy of Sciences, John Avise, argued that the evolution of the species is not by chance and that the evolution of complexity is not a problem because high fitness, point mutations are fixed in populations of bacteria in a test tube. You might think that such erroneous claims must be one-time blunders—mistakes that would be quickly retracted when pointed out. But this is not the case. These are standard evolutionary arguments. Avise’s book was endorsed by several evolutionists, and when I pointed out these enormous blunders other evolutionists rushed to his defense. Fallacious thinking is fundamental to evolutionary thought. But why? After all, evolutionists such as Avise are certainly not intellectually lacking. Evolutionists are smart, well educated and informed. So why the blatantly erroneous claims? The answer, as usual, comes down to religion.

In his book Inside the Human Genome, John Avise discusses at length the evils and inefficiencies of the world, and in particular in the genome. He explains repeatedly that this cannot be reconciled with a good god. For example, Avise introduces the reader to this problem on the third page of the book:

This is the persistent dilemma of theology. Why does suffering exist in a world governed by a loving deity? Put more simply, why do bad things happen to good (as well as bad) people? … Why for example must countless people endure sometimes lifelong pain and suffering from inherited physical disabilities? And why must the persecutions extend even to those who surely must be innocent in God’s eyes, such as the untold numbers of human embryos and fetuses who spontaneously abort in utero? Indeed, in a world run by a loving Creator God, why are senescence and death the unavoidable fates of anyone fortunate enough to have survived all of life’s earlier challenges? … But what about the evil visited upon people in situations where free will is irrelevant? The victim of a tornado or earthquake presumably had no control over such natural catastrophes, nor did an aborted embryo have control over the inherited disabilities that may have caused its premature death. [Inside the Human Genome, Oxford, 2010, p. 3-5]

This sentiment continues as Avise rehearses, later in the chapter, the standard evolutionary metaphysics that it is not the good designs that rebuke creationism so much as the harmful ones:

At least at a superficial explanatory level, evolutionary and creationist scenarios both seem plausible, in principle, for complex traits that perform their functions well. A more acid test comes from complex traits that are harmful to their bearers. As we will see in later chapters, many complex generic traits (such as pseudogenes and mobile elements) that often are functionless or even detrimental to the organisms that house them are rampant in the genomes of vertebrate animals, humans included. Did a Creator God repeat these apparent errors of genomic construction time and time again? Or are such genomic flaws merely the footprints of phylogenetic history? [28-9]

It is these harmful and inefficient designs, particularly in the genome, that Avise will elaborate on in the remainder of the book. For instance consider harmful mutations. Avise believes it would be blasphemous to ascribe them to God:

Few people would blame a loving and all-powerful God for purposefully inventing deleterious mutations; that would be blasphemous. [65]

For as Avise points out these mutations can be devastating:

most de novo mutations range from neutral to highly deleterious for human health, and collectively they leave in their wake countless shattered bodies and destroyed lives (including those of untold numbers of early human embryos). These are probably not the kinds of biological outcomes that one would wish to attribute to the direct hand of an all-powerful and loving God. [72]

It’s all about religion. It did not begin with Darwin, and ever since Darwin the religious control of science has become even stronger. Of course evolution must be a fact—our religion demands it. For otherwise we commit blasphemy. Never mind that it makes no sense scientifically. Like a Trojan Horse, religion has infected science, and it has gone viral.

Now they’re calling it “displacement.” An ubiquitous and fundamental DNA binding protein is missing from a heat-loving single cell organism. Instead, there is a novel protein in its place:

The crystal structure of Ttx1576 reveals a unique fold and a mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper.

The evolutionary tree failed yet again so evolutionists just invented another just-so story. That ubiquitous and fundamental protein was “displaced”:

ThermoDBP appears to have displaced the canonical SSB during the diversification of the Thermoproteales, a highly unusual example of the loss of a “ubiquitous” protein during evolution.

I guess anything can happen “during evolution.” As one of the evolutionists explained:

All cells, whether they are microbial or human, have some things in common. These are the fundamental components or building blocks which were present in the first cells and have been passed on over 3.5 billion years. However, we have discovered that a gene normally thought to be absolutely essential and conserved throughout every form of life, is in fact lost in one group of volcanic bugs, and replaced by a completely novel gene we have christened ThermoDBP.

As one writer explained, “The discovery has ramifications for understanding about how life has evolved on earth.” That would be an understatement. What the new discovery and associated just-so story reveal, yet again, is that pretty much anything goes “during evolution.” This is not a theory, it is a tautology. It doesn’t explain nature, it is explained by nature. Whatever evolutionists find, it must have evolved. Of course there is no scientific explanation for how novel proteins could arise. In fact even the best just-so story is a ridiculous 27 orders of magnitude short of reality. Evolutionists have no idea how it could have happened, but they are absolutely sure that it did happen: “Evolution is a fact, don’t confuse me with the facts.”

Sunday, June 10, 2012

An obvious problem with evolution is its claim that complex designs arose spontaneously. Imagine some spark plugs, valves and other assorted mechanical parts coming together to form an engine. It’s unlikely no matter how many years you have. What evolutionists would need to show is that there is a long, long sequence of simpler, intermediate designs which gradually lead from a lifeless warm little pond to the incredible species in today’s world. Of course they have shown no such thing—not even close. So instead evolutionists use sophistry—explanations that are so flawed and illogical they cannot even be said to be wrong. For example, professor and National Academy of Sciences member John Avise makes this argument:

Another ID sentiment is that the emergence of biotic complexity via natural processes (unlike under intelligent auspices) is highly improbable, a notion that proponents of ID sometimes claim to document statistically. An undisputed law of statistics states that the probability of the joint occurrence of two or more independent events is calculated by multiplying together the separate probabilities of those events. For example, suppose that independent events A and B occur with random probabilities of 1 in 10 million (i.e., 10^-7) and 1 in 100 million (10^-8), respectively. The probability that both events occur together, by chance, is thus minuscule: one in a quadrillion (i.e., 10^-7 x 10^-8 = 10^-15). Mutations are examples of such rare and independent events, each typically occurring at a rate of about 10^-7 or 10^-8 per gene per generation. Suppose that a complex adaptation (such as a metabolic resistance to two different categories of otherwise lethal drugs) requires the joint presence in an organism of two mechanistically independent mutations. A proponent of ID might conclude that this adaptation is effectively unachievable by natural forces because its random probability is so very low. Divine intervention then becomes the default explanation.

But this is a gross misapplication of statistics, as the following example will illustrate. Consider a small colony of a billion bacterial cells, housed in a test tube, that lacks the genetic capacity to survive the antibiotics penicillin and streptomycin. New mutations for penicillin resistance (p+) and streptomycin resistance (s+) are known to arise randomly in bacteria, at low frequency. If the mutation rate to p+ is a plausible 10^-7, then a culture of 10^9 bacteria should by chance contain about 100 cells with penicillin resistance. When penicillin is added to the culture, all bacteria die except for those lucky 100 cells which then quickly divide and multiply to bring their number back up to a billion cells (all now carrying the p+ mutation). In this new colony, about 10 cells should by chance be resistant to streptomycin, assuming that the mutation rate to s+ is a plausible 10^-8. If streptomycin is then added to the culture, all of the bacteria die except for these 10 cells, which again divide and multiply to repopulate the test tube with a billion descendants (all of which are now p+ and s+ jointly). By this stepwise process, the unconscious operation of selection has made virtually inevitable what might otherwise have been deemed impossible—the evolution of a complex adaptation. [Inside the Human Genome, Oxford, 2010, p. 33-5]

The logic here is astonishing. In the hands of the evolutionist a failure of his theory is transformed into a victory with what can only be described as sheer absurdity. The underlying, unspoken, premise is that the stepwise fixation of single, high fitness, point mutations is no different than the evolution of all biological complexities. In fact there are precisely zero such designs that are known to be constructable via such a sequence. Indeed, quite the opposite, science points us in the opposite direction. Even the evolution a single protein falls 27 orders of magnitude short of reality, and that is according to evolutionist’s own, outrageously optimistic assumptions.

Avise’s argument is simply jaw-dropping. It is a complete misrepresentation of what we know from science.

The whole point of evolution—that the species arose all by themselves—is also the whole problem. Evolutionists wax eloquently about how there is no goal, plan or purpose to the world. Biology arose by chance events, such as random mutations, which did not have the species in mind. But how could the species possibly arise by chance? Such a proposition is highly unlikely, to put it kindly. How do evolutionists explain this probability dilemma? How do they explain away something that is astronomically unlikely? Simple. Evolutionists say the question has got it all wrong, for the evolution of the species is not, in fact, by chance at all. Yes, there are random events involved, such as mutations, but they must pass the test of natural selection which very much is not random. But this is yet another evolutionary blunder. Not only is it a misrepresentation of evolutionary theory, it fails to resolve the probability dilemma.

The University of California Museum of Paleontology’s website about evolution, funded by your tax dollars, claims that it is a misconception that evolution means that the species arose by chance. Here is how the website explains this supposed misconception:

Chance is certainly a factor in evolution, but there are also non-random evolutionary mechanisms. Random mutation is the ultimate source of genetic variation, however natural selection, the process by which some variants survive and others do not, is not random.

In other words, yes mutations are random, but natural selection is not. This blunder is elaborated by University of California professor and National Academy of Sciences member, John Avise. Avise repeats the argument that natural selection is not random, but he also argues that the biological variation, which is subject to selection, is also, ultimately, not random:

Advocates of Intelligent Design contend that complex biological features cannot arise by chance, the implication being that chance equates to natural evolutionary processes and anti-chance equates to sentient forces. From a scientific vantage, however, the driving force of adaptive evolution—natural selection—is itself the antithesis of chance. …

Natural selection can sift only among the genetic variants available for its scrutiny, and two of the three primary sources of genetic variability—de novo mutations and recombination—occur essentially at random with respect to forging adaptations. … In this important sense, the genetic fodder upon which natural selection acts can indeed be characterized as stochastic or chancy in origin.

The third source of population genetic variation entails a mixture of “chance and necessity.” Apart from de novo mutations and recombinant genotypes, the genetic variety available for natural selection in any generation is also a function of historical circumstance, that is, of idiosyncratic genealogical outcomes that have been affected by both stochastic and directive evolutionary processes across all prior generations. Evolution going forward can work only with the biological substrates provided by evolution foregone. These biological substrates—“ghosts of evolution past”—are not supernatural legacies, but instead they are real genetic lineages and real species that have been subjected for eons to the full panoply of evolutionary processes including natural selection (the directive agent of adaptive evolution) as well as idiosyncratic mutation, recombination, and genetic drift (stochastic forces in the sense described above). [Inside the Human Genome, Oxford, 2010, p. 27-8]

Avise’s mental gymnastics are painful to watch. This blunder is consistent amongst evolutionists, but no less astonishing. First let’s consider the claim that natural selection means the origin of species wasn’t by chance. Imagine a friend wins a one-in-a-million jackpot at roulette, but he claims it wasn’t by chance because he also had some losing bets. On his losing bets he collected nothing, but on his winning bets collected his winnings. Isn’t that the very antithesis of chance?

Of course not. This is a monumental blunder in thinking. Yes he doesn’t collect on his losing bets, and he does collect on his winning bets. But that does not change the fact that roulette is a game of chance. And it doesn’t change the fact that his beating the casino was unlikely.

According to evolution biological variation is random with respect to need or purpose. Natural selection doesn’t change this. It kills off the bad designs, but winning designs are nonetheless constructed by random variation—they are by chance. Every mutation and recombination event leading to whales, cherry trees and humans was, according to evolution, random. Likewise every losing design is also by chance.

In other words, some designs win and some designs lose. The process continues and the species evolve. But it is entirely by chance. The fact that some win and some lose doesn’t change this.

Avise’s second argument is that chance is also removed from the process because it is on-going, producing new species which become the basis for further evolution. This argument is equally fallacious.

A chance process that continues for awhile is still a chance process.

The evolutionary process is still by chance. If a frog evolved from an earlier amphibian—such that the evolution of frogs was limited in its possibilities—that doesn’t change the fact that the process was, from the beginning, by chance.

Every biological variation that occurs is random. Yes natural selection kills off the bad designs. And yes the process proceeds down certain pathways, producing certain species. But every species is produced by a series of random biological variations.

The origin of species by chance is unlikely. It would require a long, long series of random mutations that just happens to construct an incredible biological design. And this would have to occur repeatedly, for all of biology’s amazing designs. And in each of these long series of random mutations, there would need to be a great many—mostly undiscovered and unknown—intermediate designs. And these intermediate designs would have to be helpful to the organism.

From single proteins to cellular processes to whole organisms, the science gives little reason to think such a process is likely. Indeed the science repeatedly indicates such a process is likely to be very unlikely.

And the evolutionist’s appeal to natural selection changes none of this. Their claim that the killing off of bad designs means that the origin of species was not by chance, and that this resolves the probability dilemma, is not only false, it demonstrates an important failure in evolutionary thinking.

Friday, June 8, 2012

A recent study of how phosphate groups regulate proteins uncovered a complex network of interactions. Kinases are proteins that add a phosphate group to a molecule, such as another protein, and phosphatases are proteins that remove the phosphate group. A protein is phosphorylated when a phosphate group is attached to a hydroxyl group in the side chain of a specific and particular amino acid out of the hundreds in the protein. Such phosphorylation controls the protein’s activity, for instance by altering the protein’s shape or attracting another molecule to bind to the protein. Furthermore, the kinase and phosphatase proteins themselves are regulated. It’s just a small bit, as the study helped demonstrate, of the cell’s immensely complex regulation network. Of course this complexity was a surprise to evolutionists who expected the usual “just-add-water” version of biology. As one of the authors explained: “Our studies have revealed an intricate network of proteins within cells that is much more complex than we previously thought.” Or as one writer explained:

Scientists studying interactions between cell proteins -- which enable the cells in our bodies to function -- have shown that proteins communicate not by a series of simple one-to-one communications, but by a complex network of chemical messages. …

Researchers, including scientists from the University of Edinburgh, used advanced technology to identify hundreds of different proteins, and then used statistical analysis to identify the more important links between them, mapping almost 2000 connections in all.

Scientists expected to find simple links between individual proteins but were surprised to find that proteins were inter-connected in a complex web.

A complex web? And how did evolution create such a complex web of regulation where proteins control other proteins by adding or removing small chemical tags such as phosphate groups?

Well first there is the problem of how random change could create a protein of any kind, let alone one that performs a needed function. Then there is the problem of how evolution could stumble upon the incredibly fine-tuned functionality of adding phosphate groups to the right hydroxyl group on the right side chain of the right amino acid in the right protein. Oh and there had to be just luckily some spare phosphate groups floating around and available.

And of course after having achieved such a miracle evolution would only have progressed a tiny step in a million mile journey. For this incredible phosphorylation capability would accomplish precisely nothing. In fact without the ability to remove the phosphate group, from the right hydroxyl group on the right side chain of the right amino acid in the right protein at the right time, the phosphorylation could be disastrous. And if not disastrous it would be an incredible stroke of luck if it accomplished anything useful. It would be a miracle if it were done at the right time, and even if it was, who knows what effect it would have on whatever function the target protein just happened to have bequeathed to it by the random actions of evolution.

You see this is all a joke. A very, very, very bad joke. And we couldn’t help but be reminded of a certain letter that touched on the topic of such bad jokes:

For the message of the cross is foolishness to those who are perishing, but to us who are being saved it is the power of God. For it is written:

“I will destroy the wisdom of the wise,
And bring to nothing the understanding of the prudent.”

Where is the wise? Where is the scribe? Where is the disputer of this age? Has not God made foolish the wisdom of this world? For since, in the wisdom of God, the world through wisdom did not know God, it pleased God through the foolishness of the message preached to save those who believe. For Jews request a sign, and Greeks seek after wisdom; but we preach Christ crucified, to the Jews a stumbling block and to the Greeks foolishness, but to those who are called, both Jews and Greeks, Christ the power of God and the wisdom of God. Because the foolishness of God is wiser than men, and the weakness of God is stronger than men.

Thursday, June 7, 2012

It has long since been known that the cells of organisms give off light but exactly how and why they do this has not been well understood. Evidence has suggested that this electromagnetic energy is more than merely a random by-product of metabolic processes but rather contains information which is transmitted and received by different cells. One recent study, for example, confirmed that some sort of non chemical information is transmitted between cells, in this case of the unicellular organism Paramecium caudatum. Different populations of the organism, separated by glass or quartz barriers which allow only certain frequencies of light, showed correlated activity. It appeared that one population can influence cell division and metabolic activities in neighboring populations. The barriers prevented any chemical influences and so information-bearing photons, rather than molecules, seem to the mechanism at work. If so, then at least two different frequencies are used in a fine-tuned electromagnetic communication system. As the paper concluded:

In the present study, three major experiments confirmed that separated populations of the ciliate Paramecium caudatuminteract with each other through glass under conditions of complete darkness. A careful control showed that the interactions are due to conspecific cells and not to the medium containing bacteria. The mutual influence between the ciliates was found for cell division, growth correlation and energy uptake (vacuole formation).

Comparing these results with corresponding studies on onion roots, yeast cells, tissue cells and zygote-germination a major common feature appears: organisms (or isolated cells) can transmit information without the use of a molecular information carrier. The observed induction on growth, furthermore, hints at a universal property of growth regulation.

If the effects on cell division (growth) found in this and other studies reveal a common feature, we are obliged to accept that cells are not only a world of effective molecules but also a world of effective light.

And this electromagnetic communication system is so sophisticated we can’t even figure it out. We don’t know how the information is generated or how the photons are transmitted or received. Even just detecting the tiny energy fluctuations is incredibly difficult.

But rest assured, evolution created all of this. Which is to say, all of this just happened to arise by itself. That’s what evolutionist insist is a fact.

What science shows, on the other hand, is that evolution is a myth. Of course that was obvious all along. Let’s be perfectly clear. We can argue over many scientific details, but what is a fact is that evolutionists dogmatically make truth claims about things they don’t even understand and cannot explain. That’s called superstition.

Wednesday, June 6, 2012

From electron microscopes to earth-orbiting observatories, scientists use a variety of instruments to study nature by measuring, observing and yes, rendering. Measurements are graphed and fitted with mathematical models. Renderings, on the other hand, are not so easily quantified. This can make them less useful for the business of building quantitative models and making predictions. But renderings can, in an instant, convey a powerful message. A picture, as they say, is worth a thousand words.

Consider, for instance, ribonuclease A, an enzyme that voraciously chops up RNA molecules. In the mid twentieth century scientists figured out how to determine the structure of such proteins using X-rays, and then later using other techniques as well. A protein sample is carefully crystallized and then exposed to an X-ray beam. The X-rays diffract as they pass through the sample and create a complex pattern which indicates the positions of the various atoms in the protein. Here is what the 124 amino acid ribonuclease A protein structure looks like when its many atoms are rendered in a three-dimensional graph:

As you can see, a graph of a protein’s individual atoms doesn’t tell you very much. It looks like, well, a bunch of atoms. But if we step back and consider the protein’s amino acids we see something very different. In a protein, the amino acids are sometimes wound tightly in a helix. Or they can be stretched out into a strand. These two patterns can be detected from the atomic locations and graphed. Here is the ribonuclease A structure again, but this time with these amino acid patterns rendered and their individual atoms left off the graph:

Suddenly a coherent structure is apparent.

Because ribonuclease A is such a voracious eater it sometimes needs to be turned off. Enter the ribonuclease inhibitor. Here are some different renderings of this beautiful horse-shoe shaped protein:

The ribonuclease inhibitor is shaped to dock with ribonuclease A and bring it to a halt. Here are renderings of the two proteins docked together:

Such renderings provide an immediate peek at the phenomena at work. They provide higher level information than do mere measurements. And it is interesting that these renderings were made with graphing tools that know nothing of ribonuclease A or ribonuclease inhibitors, in particular. Computer scientists have developed these powerful rendering tools based on general principles of protein structure. But these tools do nothing without the structural data provided by measurement techniques, such as X-ray diffraction.

So as with electron microscopes and astronomical observatories, these molecular tools create impressive, beautiful and meaningful renderings that are completely dependent on the measurements. The computer scientist creates the tool, but has no idea what rendering might emerge after the raw data are input.

A recent example of the power of rendering, and the importance of stepping back and choosing the right perspective, is the frog embryo’s electric face. If that sounds strange read on, for as one researcher said, “electric face” is the perfect description.

The body electric

Electricity is not just for engineers, it is crucial in biology as well. For instance, a cell contains various ionic compounds which give the cell interior a net charge. And the difference between the intracellular charge and that of the the external environment causes a voltage across the cell membrane. This membrane voltage is crucial in cellular biology. For instance, a wide variety of membrane proteins, such as channels that allow chemical in and out of the cell, are controlled by the membrane voltage. Change the voltage and you suddenly change the state of those proteins and their various actions.

Yes electricity is important in biology, but when Dany Adams left her digital camera and microscope apparatus running overnight, she had no idea what stunning electrical patterns would emerge on the frog embryo she was studying. Watch this video to learn more:

Here is a shorter video of just the embryo:

The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.”

The frog’s electric face is one of those renderings worth a thousand words. We could make detailed protein measurements showing that evolution cannot even explain how a single protein could have arisen. In fact there are 27 orders of magnitude between evolution’s expectations and reality. And that is going by the evolutionist’s own reckoning (in reality it is 100+ orders of magnitude). Or we could make detailed measurements of mutations and show that unicellular organisms are not likely to evolve spontaneously into elephants.

But the frog’s electric face, in an instant, reminds one of the utter absurdity of evolution. Religion drives science, and it matters.

Monday, June 4, 2012

The Epicureans called them “veering atoms” and evolutionists updated it to “random mutations.” One way or another, man must have an evolutionary narrative. But it makes no sense on the science and so, to match the mythology with the evidence, evolution must become the master craftsman. Its latest wizardry is a “risk management strategy,” as a new paper explains. Furthermore, mutation rates have been “evolutionarily optimized.” Unbelievable. The evolutionist’s just-so stories continue to become even more ridiculous. Evolution is now so brilliant that we are supposed to believe that it created the means not only to control mutation rates, but to optimize the mutation rates as well.

First, if evolution is true, we must believe that the basic mutation rate varies by more than an order of magnitude in different bacteria:

Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases.

The next result is that, under evolution, the variation between different mutation rates must not be random, but rather must follow a rational pattern:

Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection.

And so, given evolution, we must conclude that evolution has optimized the mutation rate:

Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations.

Of course there is no known mechanism that could do this:

Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved.

But evolutionists will think of something, no matter how speculative.

The findings have important implications for our understanding of evolution and the control of mutations.

In other words, results that rebuke a fundamental concept of evolution, and that cannot even be explained by evolutionists (who are notorious for being able to explain anything with their just-so stories), are presented by evolutionists as important findings for understanding how evolution works. It is all about those veering atoms.

As we saw in the previous post the cell membrane has been found to be increasingly sophisticated. Not only is the protein-punctuated sandwich structure incredibly complicated, but organisms actively fine-tune its design as conditions change. For instance, the number and location of carbon-carbon double bonds, in the phospholipid tails in the lipid bilayer, are astonishingly modified in real-time to deal with temperature changes. A recent paper agreed that “the membrane is a biological device of a staggering complexity”:

A topologically closed membrane is a ubiquitous feature of all cellular life forms. This membrane is not a simple lipid bilayer enclosing the innards of the cell: far from that, even in the simplest cells, the membrane is a biological device of a staggering complexity that carries diverse protein complexes mediating energy-dependent – and tightly regulated - import and export of metabolites and polymers.

And how could it have evolved? The paper agrees that “the origin(s) of the membrane(s) and membrane proteins remain enigmatic”

Studies of the past several decades have provided major insights into the structural organization of biological membranes and mechanisms of many membrane molecular machines. However, the origin(s) of the membrane(s) and membrane proteins remain enigmatic.

Indeed, such evolution is downright obscure:

Despite the growing understanding of the structural organization of membranes and molecular mechanisms of many membrane proteins, the origin(s) of biological membranes remain obscure.

And this is only the beginning. The paper is loaded with preposterous just-so stories, many of them contradictory, of how evolutionists believe the membrane evolved. Calling all of this raw speculation would be kind. The evolution of the cell membrane is downright ridiculous but evolutionists, as usual, remain ever dogmatic. They may not know of evolution occurred, but they’re sure it did. What’s worse, they insist it is a fact that is beyond any reasonable doubt. It would be perverse, as they often say, even to consider the possibility it may be wrong. All one needs to do is listen to evolutionists to understand what it is all about, and it isn’t science.

Sunday, June 3, 2012

The membrane that surrounds and encapsulates living cells is truly amazing. This lipid bilayer-protein mixture, which is only a few nanometers thick, has complex chemical, structural and electrical properties which are finely-tuned and crucial for the cell’s operation. And the various proteins perform a great diversity of tasks, ranging from transmitting information to transporting molecules, across the membrane. As usual the inexorable march of science continues to reveal the sophistication and elegance of the membrane design. A recent study, for instance, revealed that the membrane proteins are arranged in complex patterns, ranging from what has been described as “patches” to “networks.” Furthermore, the all-important lipid composition of the membrane strongly influences these patterns as well as the protein sequences themselves. This work reveals far greater structure and organization in the cell membrane than was previously understood. And it continues to reveal how unlikely it is that such designs spontaneously arose. For more interesting details on the cell membrane design, here is a post from a year ago on the fine-tuning of the membrane’s fluidity:

You learned about DNA and proteins in your high school biology class, but you may not remember much about the cell’s membrane which is based on a dynamic, fluctuating sandwich structure. This cellular envelope controls what chemicals enter and exit the cell, partly due to molecular machines such as channels and pumps in the membrane, and partly due to the sandwich structure itself. This sandwich structure is a barrier to certain types of chemicals. But the membrane permeability and the operation of the molecular machines depend on the details of the sandwich structure. And as recent research has been finding, contra evolutionary expectations, organisms actively maintain and fine-tune the sandwich structure in response to environmental challenges.

The cell membrane’s sandwich structure consists of two layers facing away from each other. Each layer is made up of an array of phospholipid molecules lined up next to each other. Phospholipid molecules consist of a water-loving (or hydrophilic) head, a phosphate group, and two oily (or hydrophobic) hydrocarbon tails.

The two layers face away from each other in a tail-to-tail arrangement. This creates a very oily, low dielectric, interior of the sandwich. While small oily molecules are able to pass through this membrane structure, it is difficult for any water-loving molecule, including water itself, to pass through the barrier. So when this sandwich structure forms a closed sphere surrounding the cell, the inside compartment is separated and protected from the outer aqueous environment. But the sandwich structure is not a simple, rigid, structure. It fluctuates, and this influences the membrane performance.

At lower temperatures the sandwich structure has a more rigid, gel, phase and at higher temperatures it has a less rigid, fluid phase. As with the freezing and melting of water there is a distinct phase change, between the gel and fluid phases of the sandwich structure, which occurs over a rather narrow temperature range. This melting point temperature is strongly influenced by the degree of attraction between the adjacent phospholipid tails. Depending on the temperature and this degree of attraction, the sandwich structure may be like a gel or like a fluid, and this is important because the phase influences the membrane permeability and the membrane’s molecular machines.

Within the membrane sandwich structure, the phospholipid tails are attracted to each other via the weakest chemical force, van der Waals interactions. Unlike the stronger chemical bonds, van der Waals interactions do not arise from the trading or sharing of electrons. So how do these interactions work?

Consider two neighboring atoms. As the electrons quickly move about, uneven charge distributions can occur across the atom. One side of an atom may temporarily be positively charged, and the other side negatively charged. Such charges influence the neighboring atom. For instance, a negative charge will tend to repel the electrons of the neighboring atom causing an attractive, uneven charge distribution in that atom. The two atoms can then continue with synchronized, fluctuating charge distributions. But all of this depends greatly on the distance between the two neighboring atoms. If they are too far apart (or too close together), the entire interaction, weak as it is, becomes insignificant.

The distance between adjacent phospholipid tails depends on their shape. If the tails have two hydrogen atoms for each carbon atom, then there are no double bonds. Such saturated chains have a consistent, linear, shape and they pack tightly together at the van der Waals preferred distance.

Unsaturated chains, on the other hand, have double bonds which cause structural kinks, loose packing and therefore weaker van der Waals interactions. And the particular location of the double bond is important, as some locations disrupt the van der Waals interactions more than others.

So all of this means that the number and location of hydrogen atoms in the phospholipid tails is an important tuning parameter (there are other tuning strategies as well), determining the phase of the sandwich structure and, in turn, the cell’s membrane performance. This is particularly important for organisms that are subject to greater temperature variations, such as poikilotherms. Such temperature variations can cause unwelcome phase changes in the membrane’s sandwich structure.Physiological response to temperature change

Years ago it was thought that the various protein machines in the cell’s membrane were more or less randomly distributed. It is yet another example of the influence of evolutionary thinking on biology. If the biological world is a fluke, then aren’t biological designs, such as the cell’s membrane architecture, random?

Now we know better. The cell membrane architecture is anything but random. In fact, the attention to detail is enormous. This includes the phase of the sandwich structure and its tuning mechanisms, such as the degree to which the phospholipid tails are saturated. Here are quotes from representative research papers discussing how organisms monitor and control their membrane fluidity, particularly in response to temperature variations:

E. coli incorporates increasing proportions of saturated and long-chain fatty acids into phospholipids as growth temperature is increased. It was found that this compositional variation results in the biosynthesis of phospholipids that have identical viscosities at the temperature of growth of the cells. [link to paper]

Numerous studies have shown that fluidity is an important factor in the function of biological membranes. Changes in fluidity affect the activity of membrane-bound enzymes and the activity of transporters, as well as the permeability of membranes to nonelectrolytes, water, and cations. Given that temperature has profound effects on membrane fluidity, it is not surprising that poikilotherms adjust the composition of their membranes in ways that defend fluidity in the face of changes in body temperature. …

Although the ways in which membrane composition is altered in response to temperature are not always consistent among species, tissues, cells, or even organelles, a few important trends have emerged. One prominent response to a decrease in the body temperature of poikilotherms is an increase in the percentage of unsaturated fatty acids that make up the phospholipids. … Phospholipids with saturated fatty acids pack readily into bilayers, whereas phospholipids with unsaturated (and therefore, kinked) acyl chains tend to disrupt hydrophobic interactions among acyl chains of adjacent phospholipids. An increase in the proportion of unsaturated fatty acids thus results in an increase in membrane disorder and fluidity, which tends to oppose the ordering effect of a drop in temperature. [link to paper]

The phospholipid composition of plasma membranes from the kidney of rainbow trout, Salmo gairdneri, was determined over a period of 21 days as fish were acclimating between temperatures of 5 and 20 degrees C. Proportions of phosphatidylethanolamine (PE) were significantly higher (29.03 vs. 23.26%) in membranes of 5 degrees C- than 20 degrees C-acclimated trout [link to paper]

Our observations suggest that a physical parallel to the changes of lipid composition is the maintenance of an optimal lipid order in the hydrophobic core of the cytoplasmic membranes. It can be interpreted as a tendency of Bacillus subtilis to keep the lateral pressure in its membranes at an optimal value, independent of the temperature of cultivation. [link to paper]

Not only is the cell membrane intricate and complex (and certainly not random), but it has tuning parameters such as the degree to which the phospholipid tails are saturated. It is another example of a sophisticated biological design about which evolutionists can only speculate. Random mutations must have luckily assembled molecular mechanisms which sense environmental challenges and respond to them by altering the phospholipid population in the membrane in just the right way. Such designs are tremendously helpful so of course they would have been preserved by natural selection. It is yet another example of how silly evolutionary theory is in light of scientific facts.